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[R] Competing-risks nomogram

Firas Abdollah
Jun 24, 2011 at 7:52 am
Hi R users,

I'd like to draw a nomogram using a competing-risks regression (crr function
in R), rather than a cox regression. However, the nomogram function provided
in the Design package is not good for this purpose.
Do you have any suggestion.
I really appreciate your help

Many thanks

F.Abdollah, MD
San-Raffele hospital
Milan, Italy

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6 responses

  • Frank Harrell at Jun 24, 2011 at 11:27 am
    Replace the Design package with the rms package. Use the ordinary linear
    regression trick to predict the linear predictor from the competing risk
    regression, then use nomogram on this new model (that merely represents the
    fit of interest).
    Frank

    Firas Abdollah wrote:
    Hi R users,

    I'd like to draw a nomogram using a competing-risks regression (crr
    function in R), rather than a cox regression. However, the nomogram
    function provided in the Design package is not good for this purpose.
    Do you have any suggestion.
    I really appreciate your help

    Many thanks

    F.Abdollah, MD
    San-Raffele hospital
    Milan, Italy

    -----
    Frank Harrell
    Department of Biostatistics, Vanderbilt University
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  • Firas Abdollah at Jun 25, 2011 at 8:52 am
    Many thanks for the prompt response.
    However, I am afraid that it is not completely clear for me. I
    apologize, I am not a statistician.
    Sorry, may be what I will say make totally non sense, but what I
    understood is the following:
    Let's suppose that I need to predict cancer-specific survival using
    the variables X and Y. What I need to do is to develop a model that
    include these variables and predict cancer-specific survival using the
    competing-risks regression. Then, I shall calculate the "predictions"
    of this model at a certain time point, then I shall use these
    prediction as an "endpoint", and predict it using a linear regression
    model that include the same variables, i.e X and Y. Finally, I use the
    coefficients of this final model to develop a nomogram. Is that
    correct?

    Many thanks again




    Should I calculate the "prediction" of the competing-risks regression
    model, and then use this "prediction" as an "endpoint" and predict it
    using a linear regression by including the same variables as
    predictors?

    On Fri, Jun 24, 2011 at 1:27 PM, Frank Harrell [via R]
    wrote:
    Replace the Design package with the rms package.  Use the ordinary linear
    regression trick to predict the linear predictor from the competing risk
    regression, then use nomogram on this new model (that merely represents the
    fit of interest).
    Frank

    Firas Abdollah wrote:
    Hi R users,

    I'd like to draw a nomogram using a competing-risks regression (crr function
    in R), rather than a cox regression. However, the nomogram function provided
    in the Design package is not good for this purpose.
    Do you have any suggestion.
    I really appreciate your help

    Many thanks

    F.Abdollah, MD
    San-Raffele hospital
    Milan, Italy

    Frank Harrell
    Department of Biostatistics, Vanderbilt University

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    --
    Firas Abdollah, MD
    Dept. of Urology
    San Raffaele Hospital
    Vita-Salute University,
    Via Olgettina 60, 20132, Milan, Italy
    Tel. +39 02 2643 7286
    Fax. +39 02 2643 7298
    E-mail: fir...@...com


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  • Frank Harrell at Jun 25, 2011 at 8:00 pm
    Yes you use the linear predictor from your regression as the dependent
    variable in the rms package's ols function. You will get an R^2 of 1.0.
    You can depict the ols model with nomogram(). Note that there are so many
    statistical issues in competing risks that doing this without a statistician
    is risky.
    Frank


    -----
    Frank Harrell
    Department of Biostatistics, Vanderbilt University
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  • Firas Abdollah at Jun 25, 2011 at 9:45 pm
    Many thanks

    On Sat, Jun 25, 2011 at 10:00 PM, Frank Harrell [via R]
    wrote:
    Yes you use the linear predictor from your regression as the dependent
    variable in the rms package's ols function.  You will get an R^2 of 1.0.
     You can depict the ols model with nomogram().  Note that there are so many
    statistical issues in competing risks that doing this without a statistician
    is risky.
    Frank
    Frank Harrell
    Department of Biostatistics, Vanderbilt University

    ________________________________
    If you reply to this email, your message will be added to the discussion
    below:
    http://r.789695.n4.nabble.com/Competing-risks-nomogram-tp3621907p3625011.html
    To unsubscribe from Competing-risks nomogram, click here.


    --
    Firas Abdollah, MD
    Dept. of Urology
    San Raffaele Hospital
    Vita-Salute University,
    Via Olgettina 60, 20132, Milan, Italy
    Tel. +39 02 2643 7286
    Fax. +39 02 2643 7298
    E-mail: fir...@...com


    --
    View this message in context: http://r.789695.n4.nabble.com/Competing-risks-nomogram-tp3621907p3625088.html
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  • Rgeskus at Jun 27, 2011 at 8:08 am
    Dear Firas,

    Regression on the subdistribution hazard can be performed by fitting a
    weighted Cox model. See Geskus, Biometrics 67, p. 39-49, 2011. Hence, cph
    (and coxph) can be used directly; there is no need to use the crr function
    in cmprsk. The result from the weighted cph fit should allow you to obtain a
    nomogram for the cause-specific cumulative incidence.

    with best regards,

    Ronald Geskus
    Academic Medical Center
    Amsterdam

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  • Firas Abdollah at Jun 27, 2011 at 9:14 am
    I will try it out..Thanks a lot

    On Mon, Jun 27, 2011 at 10:08 AM, rgeskus [via R]
    wrote:
    Dear Firas,

    Regression on the subdistribution hazard can be performed by fitting a
    weighted Cox model. See Geskus, Biometrics 67, p. 39-49, 2011. Hence, cph
    (and coxph) can be used directly; there is no need to use the crr function
    in cmprsk. The result from the weighted cph fit should allow you to obtain a
    nomogram for the cause-specific cumulative incidence.

    with best regards,

    Ronald Geskus
    Academic Medical Center
    Amsterdam

    ________________________________
    If you reply to this email, your message will be added to the discussion
    below:
    http://r.789695.n4.nabble.com/Competing-risks-nomogram-tp3621907p3627184.html
    To unsubscribe from Competing-risks nomogram, click here.


    --
    Firas Abdollah, MD
    Dept. of Urology
    San Raffaele Hospital
    Vita-Salute University,
    Via Olgettina 60, 20132, Milan, Italy
    Tel. +39 02 2643 7286
    Fax. +39 02 2643 7298
    E-mail: fir...@...com


    --
    View this message in context: http://r.789695.n4.nabble.com/Competing-risks-nomogram-tp3621907p3627277.html
    Sent from the R help mailing list archive at Nabble.com.

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